Intensive DNA Replication and Metabolism during the Lag Phase in Cyanobacteria

Unlike bacteria such as Escherichia coli and Bacillus subtilis, several species of freshwater cyanobacteria are known to contain multiple chromosomal copies per cell, at all stages of their cell cycle. We have characterized the replication of multi-copy chromosomes in the cyanobacterium Synechococcus elongatus PCC 7942 (hereafter Synechococcus 7942). In Synechococcus 7942, the replication of multi-copy chromosome is asynchronous, not only among cells but also among multi-copy chromosomes. This suggests that DNA replication is not tightly coupled to cell division in Synechococcus 7942. To address this hypothesis, we analysed the relationship between DNA replication and cell doubling at various growth phases of Synechococcus 7942 cell culture. Three distinct growth phases were characterised in Synechococcus 7942 batch culture: lag phase, exponential phase, and arithmetic (linear) phase. The chromosomal copy number was significantly higher during the lag phase than during the exponential and linear phases. Likewise, DNA replication activity was higher in the lag phase cells than in the exponential and linear phase cells, and the lag phase cells were more sensitive to nalidixic acid, a DNA gyrase inhibitor, than cells in other growth phases. To elucidate physiological differences in Synechococcus 7942 during the lag phase, we analysed the metabolome at each growth phase. In addition, we assessed the accumulation of central carbon metabolites, amino acids, and DNA precursors at each phase. The results of these analyses suggest that Synechococcus 7942 cells prepare for cell division during the lag phase by initiating intensive chromosomal DNA replication and accumulating metabolites necessary for the subsequent cell division and elongation steps that occur during the exponential growth and linear phases.     

Effect of light quality on the growth and proximal composition of <Emphasis Type="Italic">Amphora</Emphasis> sp.

We determined the effects of various light spectra (white, blue, green, yellow, and Grolux) on the growth rate, proximate composition, pigment content, and cell size of the marine benthic diatom Amphora sp. during two growth phases of batch cultures. The growth rate was higher under green light and lowest with Grolux and yellow light. Cell size differed significantly between growth phases but remained unaffected by light spectra; the smallest cells were observed on the initial day of culture, whereas larger cells developed in the stationary phase under Grolux treatment. The proximate composition was modified by the light spectra and growth phase. In the exponential growth phase, the protein content was higher with yellow and white light, and lipid content peaked with Grolux. The pigment content (chlorophyll a, carotenoids) was also higher under yellow light. In the stationary growth phase, we noted a higher carbohydrate content under Grolux and yellow light. Our results show that light spectra and growth phase influence the metabolism of Amphora sp., changing its proximate composition, pigment content, growth rate, and cell size.     

Growth dynamics in relation to the production of the main cellular components in the toxic dinoflagellate Ostreopsis cf. ovata

In the last decade Ostreopsis cf. ovata blooms have been among the most intense along the entire Mediterranean coast, leading to ecological and human health problems, that are associated with the toxins (palytoxin-like compounds) produced by these algal cells. These compounds are secondary metabolites, whose rates of synthesis depend on the metabolism of their precursors. In general, growth dynamics and toxicity of dinoflagellates reflect the physiological status of the organism. The aim of the present study was to investigate the cellular production of the main biochemical compounds likely involved in the growth and toxicity dynamics of O. cf. ovata during exponential to the late stationary phase in batch cultures of an Adriatic strain. Removal of major nutrients from the medium was monitored along with concentration, biovolume and production of the main cellular components (e.g. polysaccharides, proteins, lipids and toxins). Nutrient uptake, as well as toxin production rates were calculated in the different growth periods. Nutrients (N and P) were completely depleted when cells entered stationary phase and the greatest net toxin production rate (R_TOX) occurred during the first days of growth. The various palytoxins reported a relative abundance quite stable during the different growth phases, while the total toxin cellular amount increased along the growth curve. Total and extracellular released polysaccharides, as well as the lipid content increased greatly during the stationary phase, while proteins were mainly produced by cells during the exponential phase. The continuous release of polysaccharides could facilitate cell aggregation and the formation of the benthic community during algal blooms. The trend of production of the main cellular compounds in O. cf. ovata and the growth dynamics of this species lead us to hypothesize that the fast growth of this dinoflagellate, associated with the rapid use of environmental resources (nutrients, and phosphates in particular), may be an ecological/adaptive strategy which could favor this organism in competition with other species.     

Staphylococcus aureus physiological growth limitations: insights from flux calculations built on proteomics and external metabolite data

Comparing proteomics and metabolomics allows insights into Staphylococcus aureus physiological growth. We update genome and proteome information and deliver strain-specific metabolic models for three S. aureus strains (COL, N315, and Newman). We find a number of differences in metabolism and enzymes. Growth experiments (glucose or combined with oxygen limitation) were conducted to measure external metabolites. Fluxes of the central metabolism were calculated from these data with low error. In exponential phase, glycolysis is active and amino acids are used for growth. In later phases, dehydroquinate synthetase is suppressed and acetate metabolism starts. There are strain-specific differences for these phases. A time series of 2-D gel protein expression data on COL strain delivered a second data set (glucose limitation) on which fluxes were calculated. The comparison with the metabolite-predicted fluxes shows, in general, good correlation. Outliers point to different regulated enzymes for S. aureus COL under these limitations. In exponential growth, there is lower activity for some enzymes in upper glycolysis and pentose phosphate pathway and stronger activity for some in lower glycolysis. In transition phase, aspartate kinase is expressed to meet amino acid requirements and in later phases there is high expression of glyceraldehyde-3-phosphate dehydrogenase and lysine synthetase. Central metabolite fluxes and protein expression of their enzymes correlate in S. aureus.     

Lipidomic changes during different growth stages of Nitzschia closterium f. minutissima

Ultra Performance Liquid Chromatography-Electrospray ionization-Quadrupole-Time of Flight Mass Spectrometry (UPLC-ESI-Q-TOF–MS) is a powerful lipidomic tool. In this study, we developed a UPLC/Q-TOF–MS based method to investigate the lipid metabolomic changes in different growth phases of Nitzschia closterium f. minutissima. The data classification and biomarker selection were carried out by using multivariate statistical analysis, including principal components analysis (PCA), projection to latent structures with discriminant analysis (PLS-DA), and orthogonal projection to latent structures with discriminant analysis (OPLS-DA). We discovered that the intercellular lipid metabolites were significantly different among exponential, early stationary and late stationary phases. Thirty-one lipid molecules were selected and identified as putative biomarkers, including free fatty acid, Harderoporphyrin, phosphatidylglycerol, 1,2-diacyglycerl-3-O-4′-(N,N-trimethy)-homoserine, triacylglycerol, cholesterol, sulfoquinovosyldiacylglycerol, lyso-sulfoquinovosyldiacylglycerol, monogalactosyldiacylglycerol, digalactosyldiacylglycerol and lyso-digalactosyldiacylglycerol. These lipids have been shown previously to function in energy storage, membrane stability and photosynthesis efficiency during the growth of diatoms. Further analysis on the putative biomarkers demonstrated that nitrate starvation played critical role in the transition from exponential phase to stationary phase in N. closterium. This study is the first one to explore the lipidomic changes of microalgae in different growth phases, which promotes better understanding of their physiology and ecology.     

Diurnal Variations in the Motility of Populations of Biflagellate Microalgae

The motility of microalgae has been studied extensively, particularly in model microorganisms such as Chlamydomonas reinhardtii. For this and other microalgal species, diurnal cycles are well known to control the metabolism, growth, and cell division. Diurnal variations, however, have been largely neglected in quantitative studies of motility. Here, we demonstrate using tracking microscopy how the motility statistics of C. reinhardtii are modulated by diurnal cycles. With nine independently inoculated cultures synchronized to the light-dark cycle at the exponential growth phase, we repeatedly observed that the mean swimming speed is greater during the dark period of a diurnal cycle. From this measurement, using a hydrodynamic power balance, we infer the mean flagellar beat frequency and conjecture that its diurnal variation reflects modulation of intracellular ATP. Our measurements also quantify the diurnal variations of the orientational and gravitactic transport of C. reinhardtii. We use this to explore the population-level consequences of diurnal variations of motility statistics by evaluating a prediction for how the gravitactic steady state changes with time during a diurnal cycle. Finally, we discuss the consequences of diurnal variations of microalgal motility in soil and pelagic environments.     

Identification of Growth Phases and Influencing Factors in Cultivations with AGE1.HN Cells Using Set-Based Methods

Production of bio-pharmaceuticals in cell culture, such as mammalian cells, is challenging. Mathematical models can provide support to the analysis, optimization, and the operation of production processes. In particular, unstructured models are suited for these purposes, since they can be tailored to particular process conditions. To this end, growth phases and the most relevant factors influencing cell growth and product formation have to be identified. Due to noisy and erroneous experimental data, unknown kinetic parameters, and the large number of combinations of influencing factors, currently there are only limited structured approaches to tackle these issues. We outline a structured set-based approach to identify different growth phases and the factors influencing cell growth and metabolism. To this end, measurement uncertainties are taken explicitly into account to bound the time-dependent specific growth rate based on the observed increase of the cell concentration. Based on the bounds on the specific growth rate, we can identify qualitatively different growth phases and (in-)validate hypotheses on the factors influencing cell growth and metabolism. We apply the approach to a mammalian suspension cell line (AGE1.HN). We show that growth in batch culture can be divided into two main growth phases. The initial phase is characterized by exponential growth dynamics, which can be described consistently by a relatively simple unstructured and segregated model. The subsequent phase is characterized by a decrease in the specific growth rate, which, as shown, results from substrate limitation and the pH of the medium. An extended model is provided which describes the observed dynamics of cell growth and main metabolites, and the corresponding kinetic parameters as well as their confidence intervals are estimated. The study is complemented by an uncertainty and outlier analysis. Overall, we demonstrate utility of set-based methods for analyzing cell growth and metabolism under conditions of uncertainty.     

Antioxidant defence system during exponential and stationary growth phases of Phycomyces blakesleeanus: Response to oxidative stress by hydrogen peroxide

An analysis of the components of the antioxidant defence system in exponential and stationary growth phases of filamentous fungus Phycomyces blakesleeanus and the response to the oxidative stress hydrogen peroxide were performed. There is a strong positive correlation between mycelial antioxidant capacity and the contents of gallic acid, d-erythroascorbate (d-EAA) or d-erythroascorbate monoglucoside (d-EAAG). These secondary metabolites are specifically synthesized by this fungus and reach maximal values in the stationary growth phase, suggesting that they can play some role in the antioxidant defence system of this fungus. There is a differential expression of the two more notable antioxidant activities, catalase (CAT) and superoxide dismutase (SOD), depending of the growth stage of P. blakesleeanus, CAT being expressed in the exponential and SOD in the stationary phase. Phycomyces blakesleeanus showed a high resistance to the oxidative stress caused by H₂O₂ (50 and 200 mM) which was higher in exponential phase. This higher resistance can be explained by the presence of CAT, glutathione peroxidase (GPx), and the probable contribution of glutathione-S-transferase (GST) and high levels of reduced form of glutathione (GSH). The transition to stationary phase was accompanied with a higher physiological oxidative damage illustrated by the higher protein carbonylation. In this growth stage the resistance of the fungus to the oxidative stress caused by H₂O₂ could be explained by the presence of SOD, GPx, and the probable contribution of GST as well as of secondary metabolites, mainly d-EAA and d-EAAG. These results highlight a specific response to oxidative stress by H₂O₂ depending on the growth phase of P. blakesleeanus.     

Transition from exponential to linear photoautotrophic growth changes the physiology of <Emphasis Type="Italic">Synechocystis</Emphasis> sp. PCC 6803

Phototrophic microorganisms like cyanobacteria show growth curves in batch culture that differ from the corresponding growth curves of chemotrophic bacteria. Instead of the usual three phases, i.e., lag-, log-, and stationary phase, phototrophs display four distinct phases. The extra growth phase is a phase of linear, light-limited growth that follows the exponential phase and is often ignored as being different. Results of this study demonstrate marked growth phase-dependent alterations in the photophysiology of the cyanobacterium Synechocystis sp. PCC 6803 between cells harvested from the exponential and the linear growth phase. Notable differences are a gradual shift in the energy transfer of the light-harvesting phycobilisomes to the photosystems and a distinct change in the redox state of the plastoquinone pool. These differences will likely affect the result of physiological studies and the efficiency of product formation of Synechocystis in biotechnological applications. Our study also demonstrates that the length of the period of exponential growth can be extended by a gradually stronger incident light intensity that matches the increase of the cell density of the culture.     

Pseudomonas putida KT2440 metabolism undergoes sequential modifications during exponential growth in a complete medium as compounds are gradually consumed

Pseudomonas putida is a soil bacterium with a versatile and robust metabolism. When confronted with mixtures of carbon sources, it prioritizes the utilization of the preferred compounds, optimizing metabolism and growth. This response is particularly strong when growing in a complex medium such as LB. This work examines the changes occurring in P. putida KT2440 metabolic fluxes, while it grows exponentially in LB medium and sequentially consumes the compounds available. Integrating the uptake rates for each compound at three different moments during the exponential growth with the changes observed in the proteome, and with the metabolic fluxes predicted by the iJN1411 metabolic model for this strain, allowed the metabolic rearrangements that occurred to be determined. The results indicate that the bacterium changes significantly the configuration of its metabolism during the early, mid and late exponential phases of growth. Sugars served as an energy source during the early phase and later as energy and carbon source. The configuration of the tricarboxylic acids cycle varied during growth, providing no energy in the early phase, and turning to a reductive mode in the mid phase and to an oxidative mode later on. This work highlights the dynamism and flexibility of P. putida metabolism.     

Trypanosoma cruzi Proline Transport Presents a Cell Density‐dependent Regulation

Trypanosoma cruzi, the etiological agent of Chagas disease, uses proline as its main carbon source, essential for parasite growth and stage differentiation in epimastigotes and amastigotes. Since proline is mainly obtained from extracellular medium by transport proteins, in this work we studied the regulation of the T. cruzi proline transporter TcAAAP069. Proline uptake and intracellular concentration presented oscillations during epimastigote growth phases, increasing during the early exponential phase (322 pmol/min) and decreasing to undetectable levels during the late exponential phase. Transporter expression rate correlated with proline uptake, and its subcellular localization alternated from both, the plasma membrane and close to the flagellar pocket, when the transport is higher, to only the flagellar pocket region, when the transport decreased until proline uptake and TcAAAP069 protein became undetectable at the end of the growth curve. Interestingly, when parasites were treated with conditioned medium or were concentrated to artificially increase the culture density, the proline transport was completely abolished resembling the effects observed in late exponential phase. These data highlight for the first time the existence of a density‐associated regulation of relevant physiological processes such as proline metabolism.     

Metabolic analysis of antibody producing CHO cells in fed‐batch production

Chinese hamster ovary (CHO) cells are commonly used for industrial production of recombinant proteins in fed batch or alternative production systems. Cells progress through multiple metabolic stages during fed‐batch antibody (mAb) production, including an exponential growth phase accompanied by lactate production, a low growth, or stationary phase when specific mAb production increases, and a decline when cell viability declines. Although media composition and cell lineage have been shown to impact growth and productivity, little is known about the metabolic changes at a molecular level. Better understanding of cellular metabolism will aid in identifying targets for genetic and metabolic engineering to optimize bioprocess and cell engineering. We studied a high expressing recombinant CHO cell line, designated high performer (HP), in fed‐batch productions using stable isotope tracers and biochemical methods to determine changes in central metabolism that accompany growth and mAb production. We also compared and contrasted results from HP to a high lactate producing cell line that exhibits poor growth and productivity, designated low performer (LP), to determine intrinsic metabolic profiles linked to their respective phenotypes. Our results reveal alternative metabolic and regulatory pathways for lactate and TCA metabolite production to those reported in the literature. The distribution of key media components into glycolysis, TCA cycle, lactate production, and biosynthetic pathways was shown to shift dramatically between exponential growth and stationary (production) phases. We determined that glutamine is both utilized more efficiently than glucose for anaplerotic replenishment and contributes more significantly to lactate production during the exponential phase. Cells shifted to glucose utilization in the TCA cycle as growth rate decreased. The magnitude of this metabolic switch is important for attaining high viable cell mass and antibody titers. We also found that phosphoenolpyruvate carboxykinase (PEPCK1) and pyruvate kinase (PK) are subject to differential regulation during exponential and stationary phases. The concomitant shifts in enzyme expression and metabolite utilization profiles shed light on the regulatory links between cell metabolism, media metabolites, and cell growth. Biotechnol. Bioeng. 2013; 110: 1735–1747. © 2013 Wiley Periodicals, Inc.     

Ralstonia eutropha H16 flagellation changes according to nutrient supply and state of poly(3-hydroxybutyrate) accumulation

Two-dimensional polyacrylamide gel electrophoresis (2D PAGE), in combination with matrix-assisted laser desorption ionization-time of flight analysis, and the recently revealed genome sequence of Ralstonia eutropha H16 were employed to detect and identify proteins that are differentially expressed during different phases of poly(3-hydroxybutyric acid) (PHB) metabolism. For this, a modified protein extraction protocol applicable to PHB-harboring cells was developed to enable 2D PAGE-based proteome analysis of such cells. Subsequently, samples from (i) the exponential growth phase, (ii) the stationary growth phase permissive for PHB biosynthesis, and (iii) a phase permissive for PHB mobilization were analyzed. Among several proteins exhibiting quantitative changes during the time course of a cultivation experiment, flagellin, which is the main protein of bacterial flagella, was identified. Initial investigations that report on changes of flagellation for R. eutropha were done, but 2D PAGE and electron microscopic examinations of cells revealed clear evidence that R. eutropha exhibited further significant changes in flagellation depending on the life cycle, nutritional supply, and, in particular, PHB metabolism. The results of our study suggest that R. eutropha is strongly flagellated in the exponential growth phase and loses a certain number of flagella in transition to the stationary phase. In the stationary phase under conditions permissive for PHB biosynthesis, flagellation of cells admittedly stagnated. However, under conditions permissive for intracellular PHB mobilization after a nitrogen source was added to cells that are carbon deprived but with full PHB accumulation, flagella are lost. This might be due to a degradation of flagella; at least, the cells stopped flagellin synthesis while normal degradation continued. In contrast, under nutrient limitation or the loss of phasins, cells retained their flagella.     

Bacillus amyloliquefaciens CCMI 1051in vitro activity against wood contaminant fungi

Bacillus amyloliquefaciens CCMI 1051 displays antifungal activity against surface contaminant fungi, blue stain fungi and phytopathogenic fungi. The antifungal potential ofB. amyloliquefaciens CCMI 1051 is based on the production of metabolites with antifungal activity. The activity was revealed both in the exponential growth phase and in the stationary phase, being associated both to microbial growth and to secondary metabolism.     

NMR spectroscopy based metabolic profiling of urine and serum for investigation of physiological perturbations during radiation sickness

Radiation accidents are rare events that induce radiation syndrome, a complex pathology which is difficult to treat. In medical management of radiation victims, life threatening damage to different physiological systems should be taken into consideration. The present study was proposed to identify metabolic and physiological perturbations in biofluids of mice during different phases of radiation sickness using ¹H nuclear magnetic resonance (¹H NMR) spectroscopy and pattern recognition (PR) technique. The ¹H NMR spectra of the biofluids collected from mice irradiated with 5 Gray (Gy) at different time points during radiation sickness were analysed visually and by principal components analysis. Urine and serum spectral profile clearly showed altered metabolic profiles during different phases of radiation sickness. Increased concentration of urine metabolites viz. citrate, α ketoglutarate, succinate, hippurate, and trimethylamine during prodromal and clinical manifestation phase of radiation sickness shows altered gut microflora and energy metabolism. On the other hand, serum nuclear magnetic resonance (NMR) spectra reflected changes associated with lipid, energy and membrane metabolism during radiation sickness. The metabonomic time trajectory based on PR analysis of ¹H NMR spectra of urine illustrates clear separation of irradiated mice group at different time points from pre dose. The difference in NMR spectral profiles depicts the pathophysiological changes and metabolic disturbances observed during different phases of radiation sickness, that in turn, demonstrate involvement of multiple organ dysfunction. This could further be useful in development of multiparametric approach for better evaluation of radiation damage as well as for medical management during radiation sickness.     

Timing is everything: optimizing crop yield for <Emphasis Type="Italic">Thalassiosira pseudonana</Emphasis> (Bacillariophyceae) with semi-continuous culture

There is relatively little choice in cultivation methods for growing algae outdoors, either in open pond systems or closed photobioreactors—as batch, continuous, or semi-continuous culture. Algal batch culture grown in a nutrient replete environment with adequate sunlight will become self-shaded with sufficient cell density and enter a stage in the growth dynamic known as the “phase of linear growth.” It is during this phase of linear growth that primary production is at maximum and that the highest biomass is harvested. The inherent problem with batch culture is that the exponential (and possibly lag) phases necessary to achieve densities required prior to the phase of linear growth consume time and waste surface area, and thereby make this an inefficient method to grow algae. Semi-continuous culture can be forced into shade-limiting conditions by reducing growth rate from maximum through dilution, whereby phases of lag and exponential growth are skipped, and culture growth is put into a state similar to a perpetual phase of linear growth with an appropriate culture harvest/dilution cycle. Importantly, semi-continuous culture can increase net growth efficiency over batch culture when compared by shade-limited growth rate. However, scientific study and theory covering shade-limited algal growth under semi-continuous culture conditions are nearly non-existent, which currently makes its application to phycological technologies impractical through “hit and miss” strategies. This laboratory study compares shade-limited growth dynamics for batch and semi-continuous cultures of Thalassiosira pseudonana (small-sized, marine diatom). Theory for optimizing production of mass algal culture with semi-continuous culture technique through cycle period and harvest volume is developed, and guidelines to practical industrial applications are provided.     

Antifungal potential of extracellular metabolites produced by Streptomyces hygroscopicus against phytopathogenic fungi

Indigenous actinomycetes isolated from rhizosphere soils were assessed for in vitro antagonism against Colletotrichum gloeosporioides and Sclerotium rolfsii. A potent antagonist against both plant pathogenic fungi, designated SRA14, was selected and identified as Streptomyces hygroscopicus. The strain SRA14 highly produced extracellular chitinase and β-1,3-glucanase during the exponential and late exponential phases, respectively. Culture filtrates collected from the exponential and stationary phases inhibited the growth of both the fungi tested, indicating that growth suppression was due to extracellular antifungal metabolites present in culture filtrates. The percentage of growth inhibition by the stationary culture filtrate was significantly higher than that of exponential culture filtrate. Morphological changes such as hyphal swelling and abnormal shapes were observed in fungi grown on potato dextrose agar that contained the culture filtrates. However, the antifungal activity of exponential culture filtrates against both the experimental fungi was significantly reduced after boiling or treatment with proteinase K. There was no significant decrease in the percentage of fungal growth inhibition by the stationary culture filtrate that was treated as above. These data indicated that the antifungal potential of the exponential culture filtrate was mainly due to the presence of extracellular chitinase enzyme, whereas the antifungal activity of the stationary culture filtrate involved the action of unknown thermostable antifungal compound(s).